HEADER DNA 13-DEC-04 1Y8V TITLE CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O- TITLE 2 PROPYL THYMIDINE (T*) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(P2T)P*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CRYSTAL STRUCTURE, A-DNA, O2'-MODIFICATION, DECAMER EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA, AUTHOR 2 G.B.INAMATI,E.A.LESNIK,S.R.OWENS,B.S.ROSS,T.P.PRAKASH, AUTHOR 3 M.MANOHARAN REVDAT 2 24-FEB-09 1Y8V 1 VERSN REVDAT 1 28-JUN-05 1Y8V 0 JRNL AUTH M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA, JRNL AUTH 2 G.B.INAMATI,E.A.LESNIK,S.R.OWENS,B.S.ROSS, JRNL AUTH 3 T.P.PRAKASH,M.MANOHARAN JRNL TITL PROBING THE INFLUENCE OF STEREOELECTRONIC EFFECTS JRNL TITL 2 ON THE BIOPHYSICAL PROPERTIES OF OLIGONUCLEOTIDES: JRNL TITL 3 COMPREHENSIVE ANALYSIS OF THE RNA AFFINITY, JRNL TITL 4 NUCLEASE RESISTANCE, AND CRYSTAL STRUCTURE OF TEN JRNL TITL 5 2'-O-RIBONUCLEIC ACID MODIFICATIONS. JRNL REF BIOCHEMISTRY V. 44 9045 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15966728 JRNL DOI 10.1021/BI050574M REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 8451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 895 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3009 REMARK 3 BIN FREE R VALUE : 0.2957 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 412 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96200 REMARK 3 B22 (A**2) : -2.98500 REMARK 3 B33 (A**2) : 2.02300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CONJUGATE GRADIENT REFINEMENT USING REMARK 3 MAXIMUM LIKELIHOOD TARGET FOR AMPLITUDES REMARK 4 REMARK 4 1Y8V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NO REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8698 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 410D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%MPD, 40MM NA-CACODILATE, 12 MM REMARK 280 SPERMINE, 80MM KCL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.41550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.84100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.65700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.84100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.41550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.65700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: CHAINS A AND B FORM DUPLEX REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 [HYDROXY(METHYLENEAMINO)OXY]ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y84 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 (IMIDAZOLYL)ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y86 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 (FLUORO)ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 (TRIFLUORO)ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y9F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-ALLYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1Y9S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O- REMARK 900 PROPARGYL THYMIDINE (T*) REMARK 900 RELATED ID: 1WV5 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE REMARK 900 2'-O-BUTYL THYMINE IN PLACE OF T6, MG-FORM REMARK 900 RELATED ID: 1WV6 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE REMARK 900 2'-O-BUTYL THYMINE IN PLACE OF T6, SR-FORM DBREF 1Y8V A 1 10 PDB 1Y8V 1Y8V 1 10 DBREF 1Y8V B 11 20 PDB 1Y8V 1Y8V 11 20 SEQRES 1 A 10 DG DC DG DT DA P2T DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA P2T DA DC DG DC MODRES 1Y8V P2T A 6 DT 2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE MODRES 1Y8V P2T B 16 DT 2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE HET P2T A 6 24 HET P2T B 16 24 HETNAM P2T 2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE FORMUL 1 P2T 2(C13 H21 N2 O9 P) FORMUL 3 HOH *119(H2 O) LINK O3' DA A 5 P P2T A 6 1555 1555 1.61 LINK O3' P2T A 6 P DA A 7 1555 1555 1.61 LINK O3' DA B 15 P P2T B 16 1555 1555 1.60 LINK O3' P2T B 16 P DA B 17 1555 1555 1.61 CRYST1 24.831 45.314 45.682 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.040272 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021890 0.00000 MASTER 238 0 2 0 0 0 0 6 0 0 0 2 END